Job ID = 14170595 SRX = SRX8497052 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15862149 spots for SRR11952651/SRR11952651.sra Written 15862149 spots for SRR11952651/SRR11952651.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171172 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:56:08 15862149 reads; of these: 15862149 (100.00%) were paired; of these: 1247876 (7.87%) aligned concordantly 0 times 9154759 (57.71%) aligned concordantly exactly 1 time 5459514 (34.42%) aligned concordantly >1 times ---- 1247876 pairs aligned concordantly 0 times; of these: 305097 (24.45%) aligned discordantly 1 time ---- 942779 pairs aligned 0 times concordantly or discordantly; of these: 1885558 mates make up the pairs; of these: 1102419 (58.47%) aligned 0 times 315367 (16.73%) aligned exactly 1 time 467772 (24.81%) aligned >1 times 96.53% overall alignment rate Time searching: 00:56:09 Overall time: 00:56:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1425232 / 14864803 = 0.0959 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 08:36:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 08:36:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:36:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:36:11: 1000000 INFO @ Sat, 11 Dec 2021 08:36:21: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 08:36:30: 3000000 INFO @ Sat, 11 Dec 2021 08:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 08:36:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:36:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:36:39: 4000000 INFO @ Sat, 11 Dec 2021 08:36:42: 1000000 INFO @ Sat, 11 Dec 2021 08:36:49: 5000000 INFO @ Sat, 11 Dec 2021 08:36:53: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 08:36:58: 6000000 INFO @ Sat, 11 Dec 2021 08:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 08:37:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:37:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:37:05: 3000000 INFO @ Sat, 11 Dec 2021 08:37:09: 7000000 INFO @ Sat, 11 Dec 2021 08:37:14: 1000000 INFO @ Sat, 11 Dec 2021 08:37:17: 4000000 INFO @ Sat, 11 Dec 2021 08:37:19: 8000000 INFO @ Sat, 11 Dec 2021 08:37:28: 2000000 INFO @ Sat, 11 Dec 2021 08:37:28: 5000000 INFO @ Sat, 11 Dec 2021 08:37:28: 9000000 INFO @ Sat, 11 Dec 2021 08:37:38: 10000000 INFO @ Sat, 11 Dec 2021 08:37:40: 6000000 INFO @ Sat, 11 Dec 2021 08:37:41: 3000000 INFO @ Sat, 11 Dec 2021 08:37:48: 11000000 INFO @ Sat, 11 Dec 2021 08:37:52: 7000000 INFO @ Sat, 11 Dec 2021 08:37:55: 4000000 INFO @ Sat, 11 Dec 2021 08:37:58: 12000000 INFO @ Sat, 11 Dec 2021 08:38:04: 8000000 INFO @ Sat, 11 Dec 2021 08:38:07: 13000000 INFO @ Sat, 11 Dec 2021 08:38:09: 5000000 INFO @ Sat, 11 Dec 2021 08:38:15: 9000000 INFO @ Sat, 11 Dec 2021 08:38:17: 14000000 INFO @ Sat, 11 Dec 2021 08:38:23: 6000000 INFO @ Sat, 11 Dec 2021 08:38:26: 10000000 INFO @ Sat, 11 Dec 2021 08:38:27: 15000000 INFO @ Sat, 11 Dec 2021 08:38:37: 16000000 INFO @ Sat, 11 Dec 2021 08:38:37: 7000000 INFO @ Sat, 11 Dec 2021 08:38:38: 11000000 INFO @ Sat, 11 Dec 2021 08:38:47: 17000000 INFO @ Sat, 11 Dec 2021 08:38:49: 12000000 INFO @ Sat, 11 Dec 2021 08:38:51: 8000000 INFO @ Sat, 11 Dec 2021 08:38:57: 18000000 INFO @ Sat, 11 Dec 2021 08:39:01: 13000000 INFO @ Sat, 11 Dec 2021 08:39:05: 9000000 INFO @ Sat, 11 Dec 2021 08:39:06: 19000000 INFO @ Sat, 11 Dec 2021 08:39:13: 14000000 INFO @ Sat, 11 Dec 2021 08:39:17: 20000000 INFO @ Sat, 11 Dec 2021 08:39:19: 10000000 INFO @ Sat, 11 Dec 2021 08:39:24: 15000000 INFO @ Sat, 11 Dec 2021 08:39:28: 21000000 INFO @ Sat, 11 Dec 2021 08:39:32: 11000000 INFO @ Sat, 11 Dec 2021 08:39:36: 16000000 INFO @ Sat, 11 Dec 2021 08:39:38: 22000000 INFO @ Sat, 11 Dec 2021 08:39:46: 12000000 INFO @ Sat, 11 Dec 2021 08:39:47: 17000000 INFO @ Sat, 11 Dec 2021 08:39:48: 23000000 INFO @ Sat, 11 Dec 2021 08:39:58: 24000000 INFO @ Sat, 11 Dec 2021 08:39:58: 18000000 INFO @ Sat, 11 Dec 2021 08:40:00: 13000000 INFO @ Sat, 11 Dec 2021 08:40:08: 25000000 INFO @ Sat, 11 Dec 2021 08:40:10: 19000000 INFO @ Sat, 11 Dec 2021 08:40:14: 14000000 INFO @ Sat, 11 Dec 2021 08:40:18: 26000000 INFO @ Sat, 11 Dec 2021 08:40:22: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:40:28: 15000000 INFO @ Sat, 11 Dec 2021 08:40:29: 27000000 INFO @ Sat, 11 Dec 2021 08:40:34: 21000000 INFO @ Sat, 11 Dec 2021 08:40:36: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:40:36: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:40:36: #1 total tags in treatment: 13201431 INFO @ Sat, 11 Dec 2021 08:40:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:40:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:40:37: #1 tags after filtering in treatment: 11435700 INFO @ Sat, 11 Dec 2021 08:40:37: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 08:40:37: #1 finished! INFO @ Sat, 11 Dec 2021 08:40:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:40:38: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 08:40:38: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 08:40:38: start model_add_line... INFO @ Sat, 11 Dec 2021 08:40:38: start X-correlation... INFO @ Sat, 11 Dec 2021 08:40:38: end of X-cor INFO @ Sat, 11 Dec 2021 08:40:38: #2 finished! INFO @ Sat, 11 Dec 2021 08:40:38: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 08:40:38: #2 alternative fragment length(s) may be 167,598 bps INFO @ Sat, 11 Dec 2021 08:40:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.05_model.r WARNING @ Sat, 11 Dec 2021 08:40:38: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:40:38: #2 You may need to consider one of the other alternative d(s): 167,598 WARNING @ Sat, 11 Dec 2021 08:40:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:40:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:40:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:40:41: 16000000 INFO @ Sat, 11 Dec 2021 08:40:45: 22000000 INFO @ Sat, 11 Dec 2021 08:40:54: 17000000 INFO @ Sat, 11 Dec 2021 08:40:57: 23000000 INFO @ Sat, 11 Dec 2021 08:41:07: 18000000 INFO @ Sat, 11 Dec 2021 08:41:09: 24000000 INFO @ Sat, 11 Dec 2021 08:41:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:41:21: 19000000 INFO @ Sat, 11 Dec 2021 08:41:21: 25000000 INFO @ Sat, 11 Dec 2021 08:41:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:41:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:41:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.05_summits.bed INFO @ Sat, 11 Dec 2021 08:41:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2023 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:41:33: 26000000 INFO @ Sat, 11 Dec 2021 08:41:34: 20000000 INFO @ Sat, 11 Dec 2021 08:41:45: 27000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:41:48: 21000000 INFO @ Sat, 11 Dec 2021 08:41:55: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:41:55: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:41:55: #1 total tags in treatment: 13201431 INFO @ Sat, 11 Dec 2021 08:41:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:41:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:41:55: #1 tags after filtering in treatment: 11435700 INFO @ Sat, 11 Dec 2021 08:41:55: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 08:41:55: #1 finished! INFO @ Sat, 11 Dec 2021 08:41:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:41:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:41:56: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 08:41:56: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 08:41:56: start model_add_line... INFO @ Sat, 11 Dec 2021 08:41:56: start X-correlation... INFO @ Sat, 11 Dec 2021 08:41:56: end of X-cor INFO @ Sat, 11 Dec 2021 08:41:56: #2 finished! INFO @ Sat, 11 Dec 2021 08:41:56: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 08:41:56: #2 alternative fragment length(s) may be 167,598 bps INFO @ Sat, 11 Dec 2021 08:41:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.10_model.r WARNING @ Sat, 11 Dec 2021 08:41:56: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:41:56: #2 You may need to consider one of the other alternative d(s): 167,598 WARNING @ Sat, 11 Dec 2021 08:41:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:41:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:41:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:42:01: 22000000 INFO @ Sat, 11 Dec 2021 08:42:14: 23000000 INFO @ Sat, 11 Dec 2021 08:42:28: 24000000 INFO @ Sat, 11 Dec 2021 08:42:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:42:42: 25000000 INFO @ Sat, 11 Dec 2021 08:42:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:42:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:42:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.10_summits.bed INFO @ Sat, 11 Dec 2021 08:42:46: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1088 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:42:56: 26000000 INFO @ Sat, 11 Dec 2021 08:43:10: 27000000 INFO @ Sat, 11 Dec 2021 08:43:20: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:43:20: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:43:20: #1 total tags in treatment: 13201431 INFO @ Sat, 11 Dec 2021 08:43:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:43:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:43:20: #1 tags after filtering in treatment: 11435700 INFO @ Sat, 11 Dec 2021 08:43:20: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 08:43:20: #1 finished! INFO @ Sat, 11 Dec 2021 08:43:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:43:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:43:21: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 08:43:21: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 08:43:21: start model_add_line... INFO @ Sat, 11 Dec 2021 08:43:21: start X-correlation... INFO @ Sat, 11 Dec 2021 08:43:21: end of X-cor INFO @ Sat, 11 Dec 2021 08:43:21: #2 finished! INFO @ Sat, 11 Dec 2021 08:43:21: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 08:43:21: #2 alternative fragment length(s) may be 167,598 bps INFO @ Sat, 11 Dec 2021 08:43:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.20_model.r WARNING @ Sat, 11 Dec 2021 08:43:21: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:43:21: #2 You may need to consider one of the other alternative d(s): 167,598 WARNING @ Sat, 11 Dec 2021 08:43:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:43:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:43:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:43:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497052/SRX8497052.20_summits.bed INFO @ Sat, 11 Dec 2021 08:44:10: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 2 millis CompletedMACS2peakCalling